TB-Profiler result

Run: ERR12544388
Summary

Run ID: ERR12544388

Sample name:

Date: 2024-04-16T01:50:03.613174

Number of reads: 3195213

Percentage reads mapped: 99.77

Median coverage: 146.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.12 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.13 isoniazid
mshA 576488 c.1141_1143delGTGinsCC frameshift_variant&missense_variant 0.12 ethionamide Uncertain significance
isoniazid Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253274 p.Ala421Thr missense_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
embR 1416311 p.Ser346Leu missense_variant 1.0 ethambutol
embR 1417161 p.Trp63Gly missense_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170035 p.Val193Ala missense_variant 0.11 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.32 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.32 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2782774 c.1269G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448445 c.-58_*1408del transcript_ablation 0.96 ethionamide Uncertain significance
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612499 c.618C>T synonymous_variant 1.0 pyrazinamide
rpoA 3878567 c.-60C>G upstream_gene_variant 0.43 rifampicin
glpK 4139531 c.225C>T synonymous_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239281 c.-582C>G upstream_gene_variant 0.12 ethambutol
embC 4239284 c.-579C>G upstream_gene_variant 0.11 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.42 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.47 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.45 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.45 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.48 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.45 ethambutol Not assoc w R - Interim
ethR 4327964 p.Ser139Trp missense_variant 1.0 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R